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Conserved domains on  [gi|530788288|ref|NP_001269041|]
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DNA topoisomerase 3-beta-1 isoform 1 [Homo sapiens]

Protein Classification

DNA topoisomerase III( domain architecture ID 10129755)

topoisomerase III is a type 1a topoisomerase that resolves single strand DNA recombination and replication intermediates

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 172-593 1.51e-150

DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.


:

Pssm-ID: 238110 [Multi-domain]  Cd Length: 381  Bit Score: 447.44  E-value: 1.51e-150
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 172 HNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQakvntdk 251
Cdd:cd00186    1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKAFVPEDYWEIK------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 252 drsllldwdrvrvfdreiaqmflnmtklekEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQ 331
Cdd:cd00186   68 ------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEA 117

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 332 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAeGINRPRKGHDAGDHPPITPMK----SATEAELGGDAWR 407
Cdd:cd00186  118 GLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLG-RRNPKRGKKEQGAHEAIRPTKvaptPELEANLSEDEFK 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 408 LYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQ 487
Cdd:cd00186  197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE 276

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 488 TNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567
Cdd:cd00186  277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK 355

                        410       420
                 ....*....|....*....|....*.
gi 530788288 568 LNLIAQGKADYRQVLGHTLDVFKRKF 593
Cdd:cd00186  356 LDEIAEGKKDYQEVLEEFYEEFKKIV 381
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 3-167 2.83e-54

TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


:

Pssm-ID: 173782 [Multi-domain]  Cd Length: 151  Bit Score: 184.74  E-value: 2.83e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   3 TVLMVAEKPSLAQSIAKILSRGSLSSHKGLNGacsvheytgTFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAE-L 81
Cdd:cd03362    1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYY---------EFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVWPLEdP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  82 FSQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVMNkahggeKTVFRARFSSITDTDIC 161
Cdd:cd03362   72 LFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKR------KPVKRAWFSSLTPKAIR 145


                 ....*.
gi 530788288 162 NAMACL 167
Cdd:cd03362  146 RAFKNL 151
 
Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 172-593 1.51e-150

DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.


Pssm-ID: 238110 [Multi-domain]  Cd Length: 381  Bit Score: 447.44  E-value: 1.51e-150
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 172 HNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQakvntdk 251
Cdd:cd00186    1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKAFVPEDYWEIK------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 252 drsllldwdrvrvfdreiaqmflnmtklekEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQ 331
Cdd:cd00186   68 ------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEA 117

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 332 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAeGINRPRKGHDAGDHPPITPMK----SATEAELGGDAWR 407
Cdd:cd00186  118 GLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLG-RRNPKRGKKEQGAHEAIRPTKvaptPELEANLSEDEFK 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 408 LYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQ 487
Cdd:cd00186  197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE 276

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 488 TNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567
Cdd:cd00186  277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK 355

                        410       420
                 ....*....|....*....|....*.
gi 530788288 568 LNLIAQGKADYRQVLGHTLDVFKRKF 593
Cdd:cd00186  356 LDEIAEGKKDYQEVLEEFYEEFKKIV 381
PRK07219 PRK07219
DNA topoisomerase I; Validated
 3-752 4.73e-146

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 451.38  E-value: 4.73e-146
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   3 TVLMVAEKPSLAQSIAKILSRGSLS--SHKGLNgacsVHEytgtFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAE 80
Cdd:PRK07219   1 TELIIAEKNNAARRIADILSGGKAKkkRVNGVP----YYE----FERKGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAE 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  81 LFSqAPTEKKEANPklNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVmnkahgGEKTVFRARFSSITDTDI 160
Cdd:PRK07219  73 LID-ADPVKKITKQ--NYINALKKLAKDADEIIIATDYDREGELIGKEAYHILREV------CQVPVKRARFSSLTKKEI 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 161 CNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFqGKYGDLDssLISFGPCQTPTLGFCVERHDKIQSFKPETY 240
Cdd:PRK07219 144 RKAFENPDEIDFNLADAGEARQIIDLYWGAALTRFLSLSV-RQLGRWD--FLSVGRVQTPTLAFIVDREREIRAFDPEDY 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 241 WVLQAKVNTD---KDRSLLLDWDRVRVFDREIAQMFLNMTKLEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMG 317
Cdd:PRK07219 221 WKIEALLDKEaqyFYRDLIGGHEAEKFWDEEEAEEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGIS 300

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 318 PQHAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAEGINRPRKG-HDAGDHPPITPMKSA 396
Cdd:PRK07219 301 PKRAMEIAEKLYTAGYISYPRTDNTVYPDDLDPKELLKKLSKKKEYGPYAESILEQENIKPTEGkKETTDHPPIHPVDVP 380

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 397 TEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSvPLEESLPTCQRGDAF 476
Cdd:PRK07219 381 KREELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEK-FDEKELPDLEEGEKL 459

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 477 PVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTveSGRRLKPTNLGIVLVHGYYKIDAELV 556
Cdd:PRK07219 460 KVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYVI--EGDPPRPTDLGIAVIEALEKYAPEIV 537

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 557 LPTIRSAVEKQLNLIAQGKADYRQVLGHTLDVFKRKFHYFVDSIAGM-DELMEvSFSPLAATGKPLSRCGKCHRFMKYIQ 635
Cdd:PRK07219 538 SEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEIgDHLAG-SLKAENRSLKTIGKCPECGGDLIIIR 616

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 636 AKPSR--LHCS---HCDETYTLPQNGTIKL--------------------YKELRCPLDDFELvlwSSGSRGKSYPLCPY 690
Cdd:PRK07219 617 TDKGSrfVGCSgypDCRNTFPLPSTGRIKVldevcekcglpvikilrgkqTFVVGCPDCEAEK---EEEDPDEVIGPCPK 693

                        730       740       750       760       770       780       790
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530788288 691 CYNHPPFRDMKKG--MGCNEctHPSCQHSLSM-------LGIGQCVECESGVLVLDPTSGPKWKVACN-KCN 752
Cdd:PRK07219 694 CGGELAIKQLKYGsfLGCTN--YPKCKYTLPLprrgkitVTDEKCPECGLPLLRVKGGFGDELGCCNNpKCN 763
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 169-582 5.96e-140

DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.


Pssm-ID: 426069 [Multi-domain]  Cd Length: 410  Bit Score: 421.27  E-value: 5.96e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  169 EPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKygdldsSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVN 248
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLKGN------KLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  249 TDKDRSLLLDWDRVRVFDREIAQMFLNmtKLEK-EAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAER 327
Cdd:pfam01131  75 DGGGVFANAKWKRGRIFDKEEAEAILE--KLKKgTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQK 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  328 LYTQ-GYISYPRTETTHYPENFDLKGSLR-QQANHPYWADTVKRLLAEG-INRPRKGHDAGDHPPITPMKSAT-EAELGG 403
Cdd:pfam01131 153 LYEKhGLITYPRTDSTYLSDDATLKAILEyLTKNYGKYLPYAPRLLKKTkGKLTVGNAKVTAHEAIRPTGDIPvLPELSD 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  404 DAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKM 483
Cdd:pfam01131 233 DERKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKEDEEELPELKEGEELKVTQVEV 312

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  484 LEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDaELVLPTIRSA 563
Cdd:pfam01131 313 EEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVERK-KKSLVPTELGKALVEALEKFP-DLVDPELTAE 390

                         410
                  ....*....|....*....
gi 530788288  564 VEKQLNLIAQGKADYRQVL 582
Cdd:pfam01131 391 LEEKLDEIAEGKLDWKDVL 409
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 290-544 3.73e-105

Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit


Pssm-ID: 214663 [Multi-domain]  Cd Length: 259  Bit Score: 324.97  E-value: 3.73e-105
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   290 RKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHP-YWADTVK 368
Cdd:smart00437   2 EKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGkEYLDLAV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   369 RLLAEGInrPRKGHDA-GDHPPITPMKSAT----EAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCS 443
Cdd:smart00437  82 VLLKPRK--PRKGKKAqGAHEAIRPTKPIFtpelEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAK 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   444 GKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQ 523
Cdd:smart00437 160 GKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLD 239

                          250       260
                   ....*....|....*....|.
gi 530788288   524 RNYVTVEsGRRLKPTNLGIVL 544
Cdd:smart00437 240 RGYVTKK-KKKLIPTELGIAV 259
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
5-594 3.45e-94

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 306.25  E-value: 3.45e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   5 LMVAEKPSLAQSIAKILSRGslsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTLdflgkYNKWDKVDPAELFsq 84
Cdd:COG0550    3 LVIVESPAKAKTIAKYLGKD---------------------------YVVTASVGHLRDL-----PKPELDVDVENDF-- 48

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  85 APT----EKKEanPKLNMVKFLqveGRGCDYIVLWLDCDKEGENICFEVLDAVlpvmnkahGGEKTVFRARFSSITDTDI 160
Cdd:COG0550   49 EPKyeviPGKK--KQVKELKKL---AKKADEVILATDPDREGEAIAWHLLELL--------GDKKPVKRVVFNEITKKAI 115

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 161 CNAMACLGEPDHNeaLsVDA---RQELDLRIGCAFTRFQTKYFQGKygdldsslISFGPCQTPTLGFCVERHDKIQSFKP 237
Cdd:COG0550  116 KEAFKNPRDIDMN--L-VDAqqaRRILDRLVGYNLSPLLWKKVKRG--------LSAGRVQSPALRLIVEREREIEAFVP 184

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 238 ETYWVLQAKVNTDKD--RSLLLDWDRVRVFDREIAQMFLNMTKlEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLG 315
Cdd:COG0550  185 EEYWTIEATFKTGGGefTAKLVKIDGKKILDEEEAEAILAALK-GKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLG 263

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 316 MGPQHAMQTAERLYTQGYISYPRTETTHYPEnfDLKGSLRQQANhpywADTVKRLLAEGINRPRKGHDA-GDHPPITP-M 393
Cdd:COG0550  264 FSAKKTMSIAQRLYEVGLITYMRTDSVRLSE--DAVAAAREYIE----ALYGKEYLPEKPRVYKTSKNAqEAHEAIRPtG 337

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 394 KSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEE----SLPT 469
Cdd:COG0550  338 VTRTPESLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKVYGEGKDDEEEeeekRLPP 417

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 470 CQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNLGIV--- 543
Cdd:COG0550  418 LKEGEKLKLKKIEPEQHFTKPPPRYTEASLVKAMEELGIGrpsTYASI---IETLQDRGYVERE-GKRLVPTELGFIvid 493

                        570       580       590       600       610
                 ....*....|....*....|....*....|....*....|....*....|.
gi 530788288 544 LVHGYYKidaELVLPTIRSAVEKQLNLIAQGKADYRQVLGHtldvFKRKFH 594
Cdd:COG0550  494 LLEEHFP---DLVDYEFTAKMEEKLDEIAEGKLDWKDVLEE----FYKPFK 537
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 3-167 2.83e-54

TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173782 [Multi-domain]  Cd Length: 151  Bit Score: 184.74  E-value: 2.83e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   3 TVLMVAEKPSLAQSIAKILSRGSLSSHKGLNGacsvheytgTFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAE-L 81
Cdd:cd03362    1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYY---------EFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVWPLEdP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  82 FSQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVMNkahggeKTVFRARFSSITDTDIC 161
Cdd:cd03362   72 LFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKR------KPVKRAWFSSLTPKAIR 145


                 ....*.
gi 530788288 162 NAMACL 167
Cdd:cd03362  146 RAFKNL 151
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 4-155 1.42e-10

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 58.52  E-value: 1.42e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288    4 VLMVAEKPSLAQSIAKILSRGSlsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTLDFlgkynkwdkvdpaelfs 83
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGF--------------------------QAVVAVLGHLLSLEK----------------- 37

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530788288   84 qaptekkeaNPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVmnkahggEKTVFRARFSSI 155
Cdd:pfam01751  38 ---------GPKKKALKALKELALKAKEVILATDPDREGEAIALKLLELKELL-------ENAGGRVEFSEL 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
4-137 1.04e-05

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 44.17  E-value: 1.04e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288     4 VLMVAEKPSLAQSIAKILSRgslsshkglngacsvheytgtfagqpvRFKMTSVCGHVMTLDflgkynkwdkvdpaelfs 83
Cdd:smart00493   2 VLIIVEGPADAIALEKAGGK---------------------------RGNVVALGGHLLSKE------------------ 36

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 530788288    84 qaptekkeanpklnMVKFLQVEGRGCdYIVLWLDCDKEGENICFEVLDAVLPVM 137
Cdd:smart00493  37 --------------QIKLLKKLAKKA-EVILATDPDREGEAIAWELAELLKPAG 75
 
Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 172-593 1.51e-150

DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.


Pssm-ID: 238110 [Multi-domain]  Cd Length: 381  Bit Score: 447.44  E-value: 1.51e-150
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 172 HNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQakvntdk 251
Cdd:cd00186    1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKAFVPEDYWEIK------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 252 drsllldwdrvrvfdreiaqmflnmtklekEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQ 331
Cdd:cd00186   68 ------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEA 117

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 332 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAeGINRPRKGHDAGDHPPITPMK----SATEAELGGDAWR 407
Cdd:cd00186  118 GLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLG-RRNPKRGKKEQGAHEAIRPTKvaptPELEANLSEDEFK 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 408 LYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQ 487
Cdd:cd00186  197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE 276

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 488 TNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567
Cdd:cd00186  277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK 355

                        410       420
                 ....*....|....*....|....*.
gi 530788288 568 LNLIAQGKADYRQVLGHTLDVFKRKF 593
Cdd:cd00186  356 LDEIAEGKKDYQEVLEEFYEEFKKIV 381
PRK07219 PRK07219
DNA topoisomerase I; Validated
 3-752 4.73e-146

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 451.38  E-value: 4.73e-146
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   3 TVLMVAEKPSLAQSIAKILSRGSLS--SHKGLNgacsVHEytgtFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAE 80
Cdd:PRK07219   1 TELIIAEKNNAARRIADILSGGKAKkkRVNGVP----YYE----FERKGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAE 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  81 LFSqAPTEKKEANPklNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVmnkahgGEKTVFRARFSSITDTDI 160
Cdd:PRK07219  73 LID-ADPVKKITKQ--NYINALKKLAKDADEIIIATDYDREGELIGKEAYHILREV------CQVPVKRARFSSLTKKEI 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 161 CNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFqGKYGDLDssLISFGPCQTPTLGFCVERHDKIQSFKPETY 240
Cdd:PRK07219 144 RKAFENPDEIDFNLADAGEARQIIDLYWGAALTRFLSLSV-RQLGRWD--FLSVGRVQTPTLAFIVDREREIRAFDPEDY 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 241 WVLQAKVNTD---KDRSLLLDWDRVRVFDREIAQMFLNMTKLEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMG 317
Cdd:PRK07219 221 WKIEALLDKEaqyFYRDLIGGHEAEKFWDEEEAEEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGIS 300

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 318 PQHAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAEGINRPRKG-HDAGDHPPITPMKSA 396
Cdd:PRK07219 301 PKRAMEIAEKLYTAGYISYPRTDNTVYPDDLDPKELLKKLSKKKEYGPYAESILEQENIKPTEGkKETTDHPPIHPVDVP 380

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 397 TEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSvPLEESLPTCQRGDAF 476
Cdd:PRK07219 381 KREELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEK-FDEKELPDLEEGEKL 459

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 477 PVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTveSGRRLKPTNLGIVLVHGYYKIDAELV 556
Cdd:PRK07219 460 KVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYVI--EGDPPRPTDLGIAVIEALEKYAPEIV 537

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 557 LPTIRSAVEKQLNLIAQGKADYRQVLGHTLDVFKRKFHYFVDSIAGM-DELMEvSFSPLAATGKPLSRCGKCHRFMKYIQ 635
Cdd:PRK07219 538 SEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEIgDHLAG-SLKAENRSLKTIGKCPECGGDLIIIR 616

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 636 AKPSR--LHCS---HCDETYTLPQNGTIKL--------------------YKELRCPLDDFELvlwSSGSRGKSYPLCPY 690
Cdd:PRK07219 617 TDKGSrfVGCSgypDCRNTFPLPSTGRIKVldevcekcglpvikilrgkqTFVVGCPDCEAEK---EEEDPDEVIGPCPK 693

                        730       740       750       760       770       780       790
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530788288 691 CYNHPPFRDMKKG--MGCNEctHPSCQHSLSM-------LGIGQCVECESGVLVLDPTSGPKWKVACN-KCN 752
Cdd:PRK07219 694 CGGELAIKQLKYGsfLGCTN--YPKCKYTLPLprrgkitVTDEKCPECGLPLLRVKGGFGDELGCCNNpKCN 763
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 169-582 5.96e-140

DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.


Pssm-ID: 426069 [Multi-domain]  Cd Length: 410  Bit Score: 421.27  E-value: 5.96e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  169 EPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKygdldsSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVN 248
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLKGN------KLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  249 TDKDRSLLLDWDRVRVFDREIAQMFLNmtKLEK-EAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAER 327
Cdd:pfam01131  75 DGGGVFANAKWKRGRIFDKEEAEAILE--KLKKgTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQK 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  328 LYTQ-GYISYPRTETTHYPENFDLKGSLR-QQANHPYWADTVKRLLAEG-INRPRKGHDAGDHPPITPMKSAT-EAELGG 403
Cdd:pfam01131 153 LYEKhGLITYPRTDSTYLSDDATLKAILEyLTKNYGKYLPYAPRLLKKTkGKLTVGNAKVTAHEAIRPTGDIPvLPELSD 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  404 DAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKM 483
Cdd:pfam01131 233 DERKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKEDEEELPELKEGEELKVTQVEV 312

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  484 LEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDaELVLPTIRSA 563
Cdd:pfam01131 313 EEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVERK-KKSLVPTELGKALVEALEKFP-DLVDPELTAE 390

                         410
                  ....*....|....*....
gi 530788288  564 VEKQLNLIAQGKADYRQVL 582
Cdd:pfam01131 391 LEEKLDEIAEGKLDWKDVL 409
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 290-544 3.73e-105

Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit


Pssm-ID: 214663 [Multi-domain]  Cd Length: 259  Bit Score: 324.97  E-value: 3.73e-105
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   290 RKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHP-YWADTVK 368
Cdd:smart00437   2 EKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGkEYLDLAV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   369 RLLAEGInrPRKGHDA-GDHPPITPMKSAT----EAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCS 443
Cdd:smart00437  82 VLLKPRK--PRKGKKAqGAHEAIRPTKPIFtpelEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAK 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   444 GKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQ 523
Cdd:smart00437 160 GKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLD 239

                          250       260
                   ....*....|....*....|.
gi 530788288   524 RNYVTVEsGRRLKPTNLGIVL 544
Cdd:smart00437 240 RGYVTKK-KKKLIPTELGIAV 259
PRK07220 PRK07220
DNA topoisomerase I; Validated
 5-658 2.02e-101

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 331.34  E-value: 2.02e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   5 LMVAEKPSLAQSIAKILSRGSLSSHKglngACSVHEYTGTFAGQpvRFKMTSVCGHVMTLDFLGKYNKWDKVDPAELFsQ 84
Cdd:PRK07220   3 LIITEKNIAARRIAQILAPKKPKKTR----VSGVDVYRYEDNGD--DTVVVGLSGHIVNIDFPKEYNNWQKVDARDLI-D 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  85 APTEKKEANPKLnmVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVMNKAHggektVFRARFSSITDTDICNAM 164
Cdd:PRK07220  76 AEIITTPTQKKI--VTALKKLGKEADRVTIATDYDREGELIGVEALNIIKKVNPDIK-----FDRVRYSAITKKEIERAF 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 165 ACLGEPDHNEALSVDARQELDLRIGCAFTRfqtkYFQGKYGDLDSSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQ 244
Cdd:PRK07220 149 SNPVEVDFNLADAGHSRQVIDLVWGAALTR----YISLAAGRLGKMFLSVGRVQSPTLALIVDREKEREAFVPTPYWEIY 224

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 245 AKVnTDKDRSLLLDWDRVRVFDREIAQMFLNmtKLEKEAQVEATSRKEKAKQRPLALNTVEMLRvASSSLGMGPQHAMQT 324
Cdd:PRK07220 225 ATL-ENNGETFVAQHSTRRFWEKEEADRVFE--KLGKTAEVTEVEKGTKTDKPPTPFNTTEFIS-AANSIGFSAANAMRI 300

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 325 AERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYwADTVKRLLAEGINRPRKG-HDAGDHPPITPMKSATEAELGG 403
Cdd:PRK07220 301 AESLYTNGYISYPRTDNTVYPESLDLREQIEIFAEGPF-GEYAQKLLEKGELVPTRGkKETTDHPPIYPASLAKKSELKE 379

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 404 DAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWqSVPLEESLPTCQRGDAFPVGEVKM 483
Cdd:PRK07220 380 DEWKVYELVVRRFFATFAGPAEWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPY-NAPEDRLLPELSEGEELKVKKKEM 458

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 484 LEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVtveSGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSA 563
Cdd:PRK07220 459 LDKETQPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYI---HGNPIQPTNTAFAVVDALEKYAPTITKPDMTSR 535

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 564 VEKQLNLIAQGKADYRQVLGHTLDVFKRKFHYFVDSiagMDELMEVSFSPLAATgKPLSRCGKC-HRFMKYIQAKPSR-L 641
Cdd:PRK07220 536 LEEDMDKIAEGKIKEDAVLEESREMLEQVFDELDKN---REKIRESLREGLRED-KIIGKCPLCgSDLMVRRSKRGSRfI 611

                        650       660
                 ....*....|....*....|
gi 530788288 642 HCS---HCDETYTLPQNGTI 658
Cdd:PRK07220 612 GCEgypECTFSLPLPKSGQI 631
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
5-594 3.45e-94

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 306.25  E-value: 3.45e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   5 LMVAEKPSLAQSIAKILSRGslsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTLdflgkYNKWDKVDPAELFsq 84
Cdd:COG0550    3 LVIVESPAKAKTIAKYLGKD---------------------------YVVTASVGHLRDL-----PKPELDVDVENDF-- 48

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  85 APT----EKKEanPKLNMVKFLqveGRGCDYIVLWLDCDKEGENICFEVLDAVlpvmnkahGGEKTVFRARFSSITDTDI 160
Cdd:COG0550   49 EPKyeviPGKK--KQVKELKKL---AKKADEVILATDPDREGEAIAWHLLELL--------GDKKPVKRVVFNEITKKAI 115

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 161 CNAMACLGEPDHNeaLsVDA---RQELDLRIGCAFTRFQTKYFQGKygdldsslISFGPCQTPTLGFCVERHDKIQSFKP 237
Cdd:COG0550  116 KEAFKNPRDIDMN--L-VDAqqaRRILDRLVGYNLSPLLWKKVKRG--------LSAGRVQSPALRLIVEREREIEAFVP 184

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 238 ETYWVLQAKVNTDKD--RSLLLDWDRVRVFDREIAQMFLNMTKlEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLG 315
Cdd:COG0550  185 EEYWTIEATFKTGGGefTAKLVKIDGKKILDEEEAEAILAALK-GKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLG 263

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 316 MGPQHAMQTAERLYTQGYISYPRTETTHYPEnfDLKGSLRQQANhpywADTVKRLLAEGINRPRKGHDA-GDHPPITP-M 393
Cdd:COG0550  264 FSAKKTMSIAQRLYEVGLITYMRTDSVRLSE--DAVAAAREYIE----ALYGKEYLPEKPRVYKTSKNAqEAHEAIRPtG 337

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 394 KSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEE----SLPT 469
Cdd:COG0550  338 VTRTPESLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKVYGEGKDDEEEeeekRLPP 417

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 470 CQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNLGIV--- 543
Cdd:COG0550  418 LKEGEKLKLKKIEPEQHFTKPPPRYTEASLVKAMEELGIGrpsTYASI---IETLQDRGYVERE-GKRLVPTELGFIvid 493

                        570       580       590       600       610
                 ....*....|....*....|....*....|....*....|....*....|.
gi 530788288 544 LVHGYYKidaELVLPTIRSAVEKQLNLIAQGKADYRQVLGHtldvFKRKFH 594
Cdd:COG0550  494 LLEEHFP---DLVDYEFTAKMEEKLDEIAEGKLDWKDVLEE----FYKPFK 537
PRK14973 PRK14973
DNA topoisomerase I; Provisional
 5-621 6.90e-80

DNA topoisomerase I; Provisional


Pssm-ID: 184936 [Multi-domain]  Cd Length: 936  Bit Score: 277.50  E-value: 6.90e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   5 LMVAEKPSLAQSIAKILSRGSLSSHKGlNGACSVHEYTGTFAgqpvrfkmTSVCGHVMTLDFLGKYNKWDKVD--PAELF 82
Cdd:PRK14973   3 LIIAEKNIAANRIAQILAGKTKVQVKK-DGGVSTYSFDDTVV--------VGLRGHVVEVDFEPGYTNWRSEEhtPRSLI 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  83 S----QAPTEKKeanpklnMVKFLQVEGRGCDYIVLWLDCDKEGENI---CFEVLDAVLPvmnkahggEKTVFRARFSSI 155
Cdd:PRK14973  74 DadtiKKPTEKK-------IVGLIQKLAKKADRVTIATDFDTEGELIgkeAYELVRAVNP--------KVPIDRARFSAI 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 156 TDTDICNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTkyFQGKYGDldSSLISFGPCQTPTLGFCVERHDKIQSF 235
Cdd:PRK14973 139 TKEEIVTAFAEPTDLDFALAAAGEARQIIDLIWGASLTRFIS--LAAHRGG--DNILSVGRVQSPTLAMIVDREKEIEAF 214

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 236 KPETYWVLQakVNTDKD-RSLLLDWDRVRVFDREIAQMFLNMTKlekeAQVEATSRKEKAKQ--RPLALNTVEMLrVASS 312
Cdd:PRK14973 215 VPEKYWMLS--LATEKDgEGIEARHTHGRFTDSAAAEAAYDATK----EPLVVTEVKEGHKVdrAPTPFDTTTFI-VAAS 287

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 313 SLGMGPQHAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADtVKRLLAEGINRPRKGH-DAGDHPPIT 391
Cdd:PRK14973 288 RLGFSAANAMRIAEDLYMNGYISYPRTDNTIYPKSLDLNGVLATLAKGAFSKD-VAWVKDNRRPVPTRGKkSSTDHPPIH 366

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 392 PMKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWqSVPLEESLPTCQ 471
Cdd:PRK14973 367 PTGVATREELGDDRWKLYELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPY-SEAKENILPAFA 445

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 472 RGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVtveSGRRLKPTNLGIVLVHGYYKI 551
Cdd:PRK14973 446 LGEKLPILAVNLEEKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKYI---EGNPLRPTLVGRAVTESLEEH 522

                        570       580       590       600       610       620       630
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 530788288 552 DAELVLPTIRSAVEKQLNLIAQGKADYRQVLGHTLDVFKRKFHYFVDSIAGM-DELM-----EVSFSPLAATGKPL 621
Cdd:PRK14973 523 AGTITEPDMTQTLEEHMQQIKERKRTRDDVVTESRKMLHRAFDELEANEAVIgRDIMertaeELTIGPCPVCGKDL 598
PRK05776 PRK05776
DNA topoisomerase I; Provisional
 4-629 3.55e-61

DNA topoisomerase I; Provisional


Pssm-ID: 235602 [Multi-domain]  Cd Length: 670  Bit Score: 219.86  E-value: 3.55e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   4 VLMVAEKPSLAQSIAKILSRGSLSSHKGlngacSVHEYTGTFAGQpvRFKMTSVCGHVMTLDFLGK-YNKWDkVDPAELF 82
Cdd:PRK05776   3 ILVIAEKPKAARKIAEALSEKPIRCRIY-----GVPYWIVKRDGK--KIVVAPAAGHLFGLHTKSKgFPVFD-YEWKPLY 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  83 sQAPTEKKEANPKLNMVKFLqveGRGCDYIVLWLDCDKEGENICFEVLdavlpvmnKAHGGEKTVFRARFSSITDTDICN 162
Cdd:PRK05776  75 -EIDKGSKYTKKYYELLSSL---SKYADEFINACDYDIEGSVIGYLII--------KYLGDPKKAKRMKFSALTKSDIRR 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 163 AMACLGEPDHNEALSVDARQELDLRIGCAFTRFQT---KYFQGKygdldSSLISFGPCQTPTLGFCVERHDKIQSFKPET 239
Cdd:PRK05776 143 AFRNLETLDYEMINAGIARHELDWLWGINVSRALMssvRDASGK-----RVILSAGRVQSPTLKYVVEREIERNLFVPLP 217

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 240 YWVLQAKVNTdKDRSLLLDWDRVRVFDREIAQMFLNMTKLEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQ 319
Cdd:PRK05776 218 YFSVSIIIEK-NGYEFTLKYENKKFETKEEAKEILEEIKKTGYLKVTKVEVKIEILEPPPPFNLGDLQVEAARIYGFSPY 296

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 320 HAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAE--GINRPRKG-HDAGDHPPITPMKSA 396
Cdd:PRK05776 297 KTQSIAEDLYLDGLISYPRTNSQKLPPTLNIRNILKGLSRSPQYRPLVNLLLKEtkGVLKPVQGpKDDPAHPAIYPTGEP 376

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 397 TEaELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIG--PELFTCSGKTVLSPGFTEVMPWqSVPLEESLPTCQRGD 474
Cdd:PRK05776 377 PK-NLSKDEFKLYDLIVRRFLASFAAPAVLSNTIVTLRVPgfPLVFSASGQRIEERGWLKYYPF-HKFDEEELPLLKKGE 454

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 475 AFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTvESGRRLKPTNLGIVLVHGYYKIDAE 554
Cdd:PRK05776 455 RVKIVDVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYLT-SNGKYIEVTPLGFGVAEVLEKYFPD 533

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 555 LVLPTIRSAVEKQLNLIAQGKADYRQVLGHT-------LDVFKRKFHYFVDSIAGMDELMevsfsplaatgKPLSRCGKC 627
Cdd:PRK05776 534 IVSVELTRDFEEKLEMIRTGKATREEVIEEAketlnklLEEFKKNKDEIGEELAKALGLI-----------KPVGKCKIC 602


                 ..
gi 530788288 628 HR 629
Cdd:PRK05776 603 GR 604
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 3-167 2.83e-54

TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173782 [Multi-domain]  Cd Length: 151  Bit Score: 184.74  E-value: 2.83e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   3 TVLMVAEKPSLAQSIAKILSRGSLSSHKGLNGacsvheytgTFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAE-L 81
Cdd:cd03362    1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYY---------EFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVWPLEdP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  82 FSQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVMNkahggeKTVFRARFSSITDTDIC 161
Cdd:cd03362   72 LFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKR------KPVKRAWFSSLTPKAIR 145


                 ....*.
gi 530788288 162 NAMACL 167
Cdd:cd03362  146 RAFKNL 151
PRK07726 PRK07726
DNA topoisomerase 3;
1-646 3.36e-51

DNA topoisomerase 3;


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 190.76  E-value: 3.36e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   1 MKTVLmvAEKPSLAQSIAKILSrgslsSHKGLNGACSVHEYTGTFAgqpvrfkmtsvCGHVMTL----DFLGKYNKWDKV 76
Cdd:PRK07726   1 MRLFI--AEKPSVGRDIADVLK-----PHKKGDGYIEGNGYIVTWA-----------IGHLLELaepeAYDERYKRWRLE 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  77 D----PAELFSQApteKKEANPKLNMVKFL--QVegrgcDYIVLWLDCDKEGENICFEVLDAVlpvmnkahGGEKTVFRA 150
Cdd:PRK07726  63 DlpiiPEKWKLVV---KKKTAKQFNVVKKLlkQA-----TEIVIATDADREGELIAREILDYC--------GVRKPIKRL 126

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 151 RFSSITDTDICNAMACL--G---EPDHNEALsvdARQELDLRIGCAFTR-FQTKYFQGKYGDLdsslISFGPCQTPTLGF 224
Cdd:PRK07726 127 WISSLTDKAIKRAFANLkpGketIPLYYSAL---ARSRADWLVGINMTRaYTLLGRKAGYNGV----LSVGRVQTPTLAL 199

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 225 CVERHDKIQSFKPETYWVLQAKVNTDKDRSLLldW--------DRVRVFDREIAQMFLNMTKlEKEAQVEATSRKEKAKQ 296
Cdd:PRK07726 200 VVRRDEEIENFVPKPYWEVEAHLTPGERFTAK--WqpsepyqdEEGRLLDRPLAEQVVARIQ-GQPAKVTEVETKRKKEY 276

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 297 RPLALNTVEMLRVASSSLGMGPQHAMQTAERLY-TQGYISYPRTETTHYPEnfDLKGSLRQ-----QANHPYwadtvKRL 370
Cdd:PRK07726 277 APLLYDLSELQIDANKRFGLSAKETLDIAQSLYeTHKLITYPRTDSRYLPE--DMVATLPEvlnaiSKVDPY-----LLL 349

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 371 LAEGINRPRKGH---DA--GDHPPITP-MKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSG 444
Cdd:PRK07726 350 APPVLDPSIRSRawnDKkvTAHHAIIPtEQPPNLSKLSEDERKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKG 429

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 445 KTVLSPGFTEVMPWQSVPLEES--LPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLM-----------------EK 505
Cdd:PRK07726 430 KQVVEAGWKALLGKKEEDEEKEqpLPVLAKGDELKVEKGEVKEGQTQPPKRFTEGTLLSAMeniarfvqdkelkktlkET 509

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 506 HGIGTDA---SIpvhINNICQRNYVTVEsGRRLKPTNLGIVLvhgyykIDA---ELVLPTIRSAVEKQLNLIAQGKADYR 579
Cdd:PRK07726 510 DGLGTEAtraGI---IEKLFKRGYLEKK-GKYIHATDKGKQL------IDAlpeELTSPDMTAKWEQALDQISEGQLSYQ 579

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530788288 580 QvlghtldvfkrkfhyFVDSIAG-MDELME---VSFSPLAATGKPLSRCGKCHRFMKyiQAKPSRLHCSHC 646
Cdd:PRK07726 580 D---------------FMQPLKQwLKQLVEqakQSSEKYKFDNLTGPKCPDCGKPML--KVKGKNGKMLVC 633
TOPRIM_TopoIA cd01028
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 3-167 2.94e-44

TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173778 [Multi-domain]  Cd Length: 142  Bit Score: 156.23  E-value: 2.94e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   3 TVLMVAEKPSLAQSIAKILSRGSLSSHkglngacsvheytgtFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAELF 82
Cdd:cd01028    1 KVLIIAEKPSKAKTIAKILGKGSKKKG---------------FYGEGGGYVVTASVGHLLELPFPEEYVDWDKDWPLELF 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  83 sQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPvmnkahgGEKTVFRARFSSITDTDICN 162
Cdd:cd01028   66 -PFEPKYVVIPDKKKQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKC-------DNKPVKRAWFSEITPKAIRE 137


                 ....*
gi 530788288 163 AMACL 167
Cdd:cd01028  138 AFKNL 142
PRK06599 PRK06599
DNA topoisomerase I; Validated
 1-688 2.40e-37

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 149.62  E-value: 2.40e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   1 MKTVLMVAEKPSLAQSIAKILSRGslsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTLDflgkyNKWDKVDPAE 80
Cdd:PRK06599   1 MAKKLVIVESPAKAKTIKKYLGKD---------------------------YKVLASFGHVRDLP-----KKKGGVDPDN 48

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  81 LFsqAPT----EKKEanpklNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDavlpVMNKAHGGEKTVFRARFSSIT 156
Cdd:PRK06599  49 DF--APKyeiiEGKE-----KVVDALKKAAKKADAVYLATDPDREGEAIAWHIAE----VLKEAKLKDKNVKRVVFNEIT 117

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 157 DTDICNAMAclgEP-DHNEALsVD---ARQELDLRIGcaftrFQ------TKYFQGKygdldssliSFGPCQTPTLGFCV 226
Cdd:PRK06599 118 KKAVQEAIE---NPrDIDMDL-VDaqqARRALDYLVG-----FKlspllwKKVRRGL---------SAGRVQSVALRLIC 179

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 227 ERHDKIQSFKPETYWVLQAKVNTDKDRSL---LLDWD-----RVRVFDREIAQmflnmtKLEKEAQ-----VEATSRKEK 293
Cdd:PRK06599 180 EREDEIEAFIPQEYWTIEADLATSNGEPFtakLVEVNgkkleKFSITNEEQAK------ALVKALEgqaytVDKIEKKER 253

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 294 AKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLY--------TQGYISYPRTETThypenfdlkgslrqqanhpywad 365
Cdd:PRK06599 254 KRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQKLYegidlgegTVGLITYMRTDSV----------------------- 310

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 366 tvkRLLAEGINRPRK------GHD-AGDHPPI--TPMKSATEAE------------------LGGDAWRLYEYITRHFIA 418
Cdd:PRK06599 311 ---RLSNEALDEARKyitkkyGKEyLPAKPRVykKKSKNAQEAHeairptsinrtpeslkpyLTPDQFKLYELIWKRTVA 387

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 419 TVSHDCKYLQSTISF--RIGPELFTCSGKTVLSPGFTEVMPwQSVPLEES-----LPTCQRGDAFPVGEVkmLEKQ--TN 489
Cdd:PRK06599 388 SQMAPAILDQTSVDIasENGKYVFRATGSVILFPGFLKVYG-ESKDDEEEddeklLPPLKEGEKLKLDEL--LPEQhfTE 464

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 490 PPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNLG-IV---LVHGY-----YKIDAELvl 557
Cdd:PRK06599 465 PPPRYSEASLVKKLEEYGIGrpsTYASI---ISTLQDREYVELE-KKRFIPTDLGrIVndfLVEHFpkyvdYDFTAGL-- 538

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 558 ptirsavEKQLNLIAQGKADYRQVlghtLDVFKRKFHYFVDSIAGMDELMEVSFSPLAAT-----GKPLS-RCGKCHRFm 631
Cdd:PRK06599 539 -------EDELDEIAEGKKDWKPV----LREFWEPFISNLEKVEEDVRTEKVTQEETDETcpkcgGGPLVlKLGKNGKF- 606

                        730       740       750       760       770       780       790
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 632 kyiqakpsrLHCSH---CDETYTLPQNG-----TIKLYKELRCPLDDFELVLwSSGSRGK-----SYPLC 688
Cdd:PRK06599 607 ---------LGCSGypeCKYTKNITRDEdepieEEEIVEEEKCPKCGGPLVL-KKGRYGKflacsGYPEC 666
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
 108-631 1.26e-36

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 148.79  E-value: 1.26e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 108 GCDYIVLWLDCDKEGENICFEVLDaVLpvmnkaHGGEKTVFRARFSSITDTDICNAMAclgEP-DHNEALsVDA---RQE 183
Cdd:PRK07561  86 DADELYLATDPDREGEAIAWHLLE-VL------GGDDVPVKRVVFNEITKNAIQEAFE---NPrELDINL-VNAqqaRRF 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 184 LDlRIgcaftrfqtkyfqgkYGDLDSSLI--------SFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVNTDKDRSL 255
Cdd:PRK07561 155 LD-RL---------------VGYMVSPLLwkkiarglSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAF 218

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 256 LLD--------WDRVRVFDREIAQMFLnmTKLEKeAQVEATSRKEKAKQR-PLALNTVEMLRVASSS-LGMGPQHAMQTA 325
Cdd:PRK07561 219 EARlthldgkkFAPVDLLNEAQAEAAV--AALEG-ARYSVASVEDKPTTRkPSAPFTTSTLQQEASRkLGFSVKKTMRIA 295

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 326 ERLYTQGYISYPRTETTHY-PENFDlkgSLRQQANHPYWADtvkrLLAEGinrPR------KG----HDAgdhppITP-- 392
Cdd:PRK07561 296 QRLYEAGYITYMRTDSTNLsQEAIN---AARGYIGDNYGKK----YLPEK---PRqysskaKNaqeaHEA-----IRPsd 360

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 393 -MKSATE-AELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQS--VPLEES-- 466
Cdd:PRK07561 361 vFRTPDQlKGLEGDAQRLYELIWKRFVASQMAPARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYVEGRddALDDEDrr 440

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 467 LPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNLG-I 542
Cdd:PRK07561 441 LPALKVGDALTLEKLDPTQHFTKPPARYSEASLVKELEKLGIGrpsTYASI---ISTIQDRGYVRLE-NRRFYPEKMGrI 516

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 543 V--LVHGYYkidAELVLPTIRSAVEKQLNLIAQGKADYRQVlghtLDVFKRKFHYFVDSIA------GMDELMEVsfspl 614
Cdd:PRK07561 517 VtdRLEEFF---PRLVDYDFTARMEEELDDIANGEADWKPV----LDDFYKDFSQQLEKAEelreegGMRPNQMV----- 584

                        570
                 ....*....|....*...
gi 530788288 615 aatgkPLSR-CGKCHRFM 631
Cdd:PRK07561 585 -----ITDRdCPTCGRGM 597
PRK08173 PRK08173
DNA topoisomerase III; Validated
 1-647 6.97e-34

DNA topoisomerase III; Validated


Pssm-ID: 236172 [Multi-domain]  Cd Length: 862  Bit Score: 140.19  E-value: 6.97e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   1 MKTVLMVAEKPSLAQSIAKILsrGSLSSHKglngacsvhEYtgtFAGQpvRFKMTSVCGHVMTL----DFLGKYNKWD-- 74
Cdd:PRK08173   1 MSKALIIAEKPSVANDIARAL--GGFTKHD---------EY---FESD--EYVLSSAVGHLLEIaapeEYEVKRGKWSfa 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  75 --KVDPaELFSQAPTEKKEANPKLnMVKflQVEGRGCDYIVLWLDCDKEGENICFEVLDAVlpvmnkahGGEKTVFRARF 152
Cdd:PRK08173  65 hlPVIP-PHFDLNPIAKTESRLKV-LTK--LIKRKDVTRLINACDAGREGELIFRLIAQHA--------KAKKPVKRLWL 132

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 153 SSITDTDICNAMACLGEPDHNEALSvDA---RQELDLRIGCAFTRFQTKyFQGKYGDLdsSLISFGPCQTPTLGFCVERH 229
Cdd:PRK08173 133 QSMTPQAIRDGFANLRSDEDMQPLA-DAarcRSEADWLVGINGTRAMTA-FNSKGGGF--FLTTVGRVQTPTLSIVVERE 208

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 230 DKIQSFKPETYWVLQA-------------------KVNTDKDRsllldwdRV-RVFDREIAQMFLNMTKlEKEAQVEATS 289
Cdd:PRK08173 209 EKIRRFVPRDYWEVRAefvaaagfyegrwfdpkfkKDEFDPEK-------RAsRLWSEAAAEAIVAACR-GKPGTVTEES 280

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 290 rKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQ-GYISYPRTETTHYPENF--DLKGSLRQQANHPYWADT 366
Cdd:PRK08173 281 -KPSTQLSPLLFDLTSLQREANGRFGFSAKNTLGLAQALYEKhKVLTYPRTDSRALPEDYlgTVKQTLEMLKESNNYLPH 359

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 367 VKRLLAEGINRPRK----GHDAGDHPPITPM----KSATEAELggdawRLYEYITRHFIATVSHDCKYLQSTISFRIGPE 438
Cdd:PRK08173 360 AKQILDKGWVKPNKrifdNSKISDHFAIIPTlqapKSLSEPEQ-----KLYDLVVKRFLAVFFPAAEFLVTTRITEVAGH 434

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 439 LFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLME-------------- 504
Cdd:PRK08173 435 HFKTEGKVLVNPGWLAVYGKEAQGADANLVPVQKGEKVKTDKIEAVALTTKPPARYNEATLLSAMEgagklveddelrea 514

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 505 --KHGIGTDASIPVHINNICQRNYVtVESGRRLKPT----NLgIVLVHGyYKIDaELVLPTIRSAVEKQLNLIAQGK--- 575
Cdd:PRK08173 515 maEKGLGTPATRAAIIEGLLGEKYL-VREGRELIPTakafQL-MTLLRG-LGVE-ELTSPELTGEWEYKLSQIERGKlsr 590

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530788288 576 -ADYRQVLGHTLDVFKRKFHYFVDSIAGmdelmevSFSPLAAtgkPLSRCGkchrfmKYIQAKPSRLHCSHCD 647
Cdd:PRK08173 591 dAFMQEIAQMTQQIVKRAKEYDSDTIPG-------DYATLQT---PCPNCG------GVVKENYRRFACTKCD 647
TOP1Bc smart00436
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ...
 147-242 1.10e-32

Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit


Pssm-ID: 214662 [Multi-domain]  Cd Length: 89  Bit Score: 121.54  E-value: 1.10e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   147 VFRARFSSITDTDICNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYgdldsslISFGPCQTPTLGFCV 226
Cdd:smart00436   1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRNGV-------LSAGRVQTPTLGLIV 73

                           90
                   ....*....|....*.
gi 530788288   227 ERHDKIQSFKPETYWV 242
Cdd:smart00436  74 EREREIKNFVPKPYWE 89
PRK08780 PRK08780
DNA topoisomerase I; Provisional
 1-635 3.80e-31

DNA topoisomerase I; Provisional


Pssm-ID: 181555 [Multi-domain]  Cd Length: 780  Bit Score: 131.04  E-value: 3.80e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   1 MKTVLMVAEKPSLAQSIAKILSRGslsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTLdflgkYNKWDKVDPAE 80
Cdd:PRK08780   1 MSKHLVIVESPAKAKTINKYLGKD---------------------------FTVLASYGHVRDL-----VPKEGAVDPEN 48

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  81 LFSQ--APTEKKEANpklnmVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVlpvmnKAHG--GEKTVFRARFSSIT 156
Cdd:PRK08780  49 GFAMryDLIDKNEKH-----VEAIAKAAKSADDLYLATDPDREGEAISWHLAEIL-----KERGllKDKPMQRVVFTEIT 118

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 157 DTDICNAMAclgepdHNEALSVD------ARQELDLRIGCAFTRFQTKYFQgkygdldsSLISFGPCQTPTLGFCVERHD 230
Cdd:PRK08780 119 PRAIKEAMA------KPRDIASDlvdaqqARRALDYLVGFNLSPLLWRKIQ--------RGLSAGRVQSPALRMIVEREE 184

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 231 KIQSFKPETYWVLQAKVNTDKD----RSLLLDWDRVRVF---DREIAQMFLNmtKLEKEAQ----VEATSRKEKaKQRPL 299
Cdd:PRK08780 185 EIEAFIAREYWSIEADCAHPSQpfnaKLIKLDGQKFEQFtitDGDTAEAARL--RIQQAAQgtlhVTDVESKER-KRNPA 261

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 300 ALNTVEMLRV-ASSSLGMGPQHAMQTAERLY---------TQGYISYPRTETTHYPEnfDLKGSLRQQANHPYWADTVKR 369
Cdd:PRK08780 262 PPFTTSTLQQeASRKLGFTTRRTMQVAQKLYegvdlgdegSVGLITYMRTDSVNLSQ--DALAEIRDVIARDYGTASLPD 339

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 370 LLAEGINRPRKGHDAgdHPPITP---MKSATE--AELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPE-LFTCS 443
Cdd:PRK08780 340 QPNTYKTKSKNAQEA--HEAVRPtsaLRTPAQvaRFLSDDQRRLYELIWKRAVACQMIPATLNTVSVDLAAGSEhVFRAT 417

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 444 GKTVLSPGFTEVM-------PWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIG---TDAS 513
Cdd:PRK08780 418 GSTVVVPGFLAVYeegkddkSAEDEDEGRKLPPMKEGDNVPLERIRAEQHFTEPPPRYTEASLVKALEEYGIGrpsTYAS 497

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 514 IpvhINNICQRNYVTVEsGRRLKPTNLGIVlVHGY----------YKIDAELvlptirsavEKQLNLIAQGKADYRQVLG 583
Cdd:PRK08780 498 I---ISTLQFRKYVEME-GRRFRPTDVGRA-VNKFltghftryvdYDFTARL---------EDDLDAVSRGEKEWIPLME 563

                        650       660       670       680       690
                 ....*....|....*....|....*....|....*....|....*....|...
gi 530788288 584 HTLDVFKRKFHYFVDSIAGMDELMEVSFSPLAATGKPLS-RCGkchRFMKYIQ 635
Cdd:PRK08780 564 KFWGPFKELVEEKKDSVDRTEAGQVRELGTDPKSGKPVSvRIG---RFGPMVQ 613
PRK14724 PRK14724
DNA topoisomerase III; Provisional
 1-602 4.24e-23

DNA topoisomerase III; Provisional


Pssm-ID: 237803 [Multi-domain]  Cd Length: 987  Bit Score: 105.81  E-value: 4.24e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   1 MKTvLMVAEKPSLAQSIAKILS--RGSLSSHKglngacsvhEYtgtFAGQpvRFKMTSVCGHVMTL----DFLGKYNKWD 74
Cdd:PRK14724   1 TKT-LVIAEKPSVAQDIVRALTpvAGKFEKHD---------EH---FESD--SYVVTSAVGHLVEIqapeEFDVKRGKWS 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  75 ----KVDPAElFSQAPTEKKEAnpKLNMVkFLQVEGRGCDYIVLWLDCDKEGENIcFEVLDAVlpVMNKAHGGEKTVFRA 150
Cdd:PRK14724  66 fanlPVIPPY-FDLKPVDKTKT--RLNAV-VKLAKRKDVTELVNACDAGREGELI-FRLIEQY--AGGAKGGLGKPVKRL 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 151 RFSSITDTDICNAMACLGEPDHNEALSVDAR--QELDLRIGCAFTRFQTKyFQGKYGDLdsSLISFGPCQTPTLGFCVER 228
Cdd:PRK14724 139 WLQSMTPQAIRDGFDNLRSDAQMQGLASAARsrSEADWLVGINGTRAMTA-FNSRDGGF--FLTTVGRVQTPTLSLVVER 215

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 229 HDKIQSFKPETYWVLQAKVNTDKDRSL--LLD--WDRV---------RVFDREIAQMFLNMTKlEKEAQVEATSrKEKAK 295
Cdd:PRK14724 216 EEKIRKFVSRDYWEIHAGFHAEAGEYLgkWFDpqWKKAsddpearadRVWSEREARAIADAVR-GKAATVTEES-KPTTQ 293

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 296 QRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQ-GYISYPRTETTHYPEN--------FDL--KGSLRQQANHPYWA 364
Cdd:PRK14724 294 ASPLLFDLTSLQREANGKFGFSAKTTLALAQSLYERhKALTYPRTDSRALPEDylpvakqtFEMlaTSGMRHLAPFAQQA 373

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 365 dtvkrlLAEGINRPRK----GHDAGDHPPITPMKSA----TEAElggdaWRLYEYITRHFIATVSHDCKYLQST-ISFRI 435
Cdd:PRK14724 374 ------LDGNYVRPSKrifdNSKVSDHFAIIPTTQApsglSEAE-----QKLYDLVVRRFMAVFFPSAEYQVTTrISQVV 442

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 436 GPElFTCSGKTVLSPGF---------TEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLME-- 504
Cdd:PRK14724 443 GHS-FKTEGKVLVKPGWlaiygkeaaNEVEDAKDGDKGQPLVPVKPGEMVRTEFAEAKGLKTKPPARYSEATLLGAMEsa 521

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 505 --------------KHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDA-ELVLPTIRSAVEKQLN 569
Cdd:PRK14724 522 gkqidddelreamqEKGLGTPATRAAIIEGLLTEKYMLRE-GRELIPTAKAFQLMTLLRGLGVeELSRAELTGEWEYKLA 600

                        650       660       670
                 ....*....|....*....|....*....|....*..
gi 530788288 570 LIAQGK----ADYRQVLGHTLDVFKRKFHYFVDSIAG 602
Cdd:PRK14724 601 QMEKGQlsreAFMQQIAAMTEKLVKKAKEYDRDTIPG 637
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 1-589 4.02e-21

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 99.13  E-value: 4.02e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288   1 MKTVLMVAEKPSLAQSIAKILSRGslsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTL-----------DFLGK 69
Cdd:PRK06319   1 MKKSLIIVESPAKIKTLQKLLGEG---------------------------FIFASSLGHIVDLpakefgidienDFEPD 53

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288  70 YnkwdkvdpaelfsQAPTEKKEanpklnMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDaVLPVMNKahggektVFR 149
Cdd:PRK06319  54 Y-------------QILPDKEE------VINKICKLAKKCDVVYLSPDPDREGEAIAWHIAN-QLPKNTK-------IQR 106

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 150 ARFSSITDTDICNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERH 229
Cdd:PRK06319 107 ISFNAITKGAVTEALKHPREIDMALVNAQQARRLLDRIVGYKISPILSRKLQRRSG------VSAGRVQSVALKLVVDRE 180

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 230 DKIQSFKPETYWVLQAKVNTDKDRSLLL---------DWDR-----------VRVFDREIAQMFLNMtkLEKEA-QVEAT 288
Cdd:PRK06319 181 KAIEAFVPVEYWNIRVHLKDPKTQKTFWahlysvdgkKWEKeipegktedevLLINSKEKADHIVEL--LESATyTVTRV 258

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 289 SRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLY---------TQGYISYPRTETTHY-PENFD-LKGSLRQQ 357
Cdd:PRK06319 259 ESKEKRRNAYPPFITSTLQQEASRHFRFSSSRTMNIAQTLYegvdldsegATGLITYMRTDSVRTdPEALKqVRKYIEGT 338

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 358 ANHPYWADTVKRLLAEginrpRKGHDAgdHPPITPMKSATEAE-----LGGDAWRLYEYITRHFIATVSHDCKY--LQST 430
Cdd:PRK06319 339 FGKEFLPSSPNVYTTK-----KMAQDA--HEAIRPTDITLTPEklrskLTEDQYKLYSLIWKRFVASQMIPAIYdtLAIR 411

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 431 ISFRIGPELfTCSGKTVLSPGFTEV---MPWQSVPLEE--SLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEK 505
Cdd:PRK06319 412 ITTNKGIDL-RATGSLLKFKGFLAVyeeKRDDEGDEEEniHLPKLHEQDVLTKEELSAEQAFTKPLPRFTEASLVKELEK 490

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 506 HGIGTDASIPVHINNICQRNYvTVESGRRLKPTNLGIVLVHGYykidaELVLPTI-----RSAVEKQLNLIAQGKADYRQ 580
Cdd:PRK06319 491 SGIGRPSTYATIMNKIQSREY-TLKENQRLRPTELGKIISQFL-----ETNFPRImdigfTALMEDELELIADNKKPWKL 564


                 ....*....
gi 530788288 581 VLGHTLDVF 589
Cdd:PRK06319 565 LLQEFWELF 573
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
 112-573 8.78e-12

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 69.20  E-value: 8.78e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 112 IVLWLDCDKEGENICFEVLDAVLPVMNKAhggeKTVF-RARFSSITDTDICNAMA--CLGEPDHNEALSVDARQELDlRI 188
Cdd:PTZ00407 128 IILATDPDREGELIAVHALQTIKRLYPKL----KVPFsRAYMHSITEDGIRKAMRerHVEACDYDLANAAETRHAMD-RI 202

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 189 gcaftrfqtkyfqgkYGDLDSSLI--------SFGPCQTPTLGFCVERHDKIQSF--KPETYWVLQA------------- 245
Cdd:PTZ00407 203 ---------------FGFLGSSVVraansqmrSIGRVQTPALILINEREDKIKAFleSNKSTFEVQAmcqfpsphgttfs 267

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 246 ---KVNTDKdRSLLLDWDRVRVFDREIAQMFLNMT---KLEKEAQVEATsrkEKAKQRPLALNTveMLRVASSSLGMGPQ 319
Cdd:PTZ00407 268 qvvTITPDR-KGGASHWATEAEARRCLEQWKLNNCtgfSVPLEPKPQPS---VVPPPQPFTMAT--AIAKANRQLKYSSE 341

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 320 HAMQTAERLYTQGYISYPRTETTHYPENF--DLKGSLRQQANhpywadtvKRLLAEGINRPRKGHDaGDHPPITPMKSAT 397
Cdd:PTZ00407 342 MVSGCLQDLFQLGHITYPRTDSTRIDESAlpDIYAAVKKEFG--------KEFLYRLEDRTVSAQE-GKGSKKTGKKRST 412

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 398 EAELGGDAWR------------------------------LYEYITRHFIAT--VSHDCKYLQSTISFRI--GPEL-FTC 442
Cdd:PTZ00407 413 KQKKGADTPVgnvedaheairptnidttgeslslspptraVYDLVRRNTLAVfmIPMKTEKIVATVKFTSgsGEKLeFEL 492

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 443 SGKTVLSPGFTE----------------------------VMPWQS-------VPLEESLPTCQRGDAFPVGEVKMLEKQ 487
Cdd:PTZ00407 493 QGKRVVEPGWTRafhkgdkgttgpaeetdeditaveegapVVPSLSqeefkaiMNLRSQLGSGVQKGFFELRSPQVRENR 572

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288 488 TNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHgyykiDAELVLPTI-----RS 562
Cdd:PTZ00407 573 PVPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKGRCETTPVGRMLVE-----TAKSTFPSIvdigfTA 647

                        570
                 ....*....|.
gi 530788288 563 AVEKQLNLIAQ 573
Cdd:PTZ00407 648 AFEKKLDRIAK 658
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 4-155 1.42e-10

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 58.52  E-value: 1.42e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288    4 VLMVAEKPSLAQSIAKILSRGSlsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTLDFlgkynkwdkvdpaelfs 83
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGF--------------------------QAVVAVLGHLLSLEK----------------- 37

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530788288   84 qaptekkeaNPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVmnkahggEKTVFRARFSSI 155
Cdd:pfam01751  38 ---------GPKKKALKALKELALKAKEVILATDPDREGEAIALKLLELKELL-------ENAGGRVEFSEL 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
4-137 1.04e-05

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 44.17  E-value: 1.04e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530788288     4 VLMVAEKPSLAQSIAKILSRgslsshkglngacsvheytgtfagqpvRFKMTSVCGHVMTLDflgkynkwdkvdpaelfs 83
Cdd:smart00493   2 VLIIVEGPADAIALEKAGGK---------------------------RGNVVALGGHLLSKE------------------ 36

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 530788288    84 qaptekkeanpklnMVKFLQVEGRGCdYIVLWLDCDKEGENICFEVLDAVLPVM 137
Cdd:smart00493  37 --------------QIKLLKKLAKKA-EVILATDPDREGEAIAWELAELLKPAG 75
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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